Is There Any Stand Alone Dot Plot Program?

Question

[Liuyunlong]

Is there any stand alone dot plot program which is like web-based in 'Plant Genome Duplication Database' or CoGE? Maybe dotter is a candidate，but I don't like its interface.

ps:It required whole genome pep blastp hit based plot,not sequence alignment based.

Answer 1

[Haibao Tang]

I use a python script to generate dot plot, for synteny purposes. It depends on a plotting library matplotlib. Incidentally, I am involved in the two projects you mentioned.

Usage:
blast_plot.py blast_file --qbed query.bed --sbed subject.bed

visualize the blast_file in a dotplot

Options:
  -h, --help   show this help message and exit
  --qbed=QBED  path to qbed
  --sbed=SBED  path to sbed
  --synteny    run a fast synteny scan and display synteny blocks

blast_file is a BLAST tabular output (-m 8 in BLAST or -outfmt 6 in BLAST+). The .bed file has four columns.

chromosome_id    start    stop    gene_name

The gene names in query.bed has to match the names used in the first column in blast_file; names in subject.bed has to match names in the second column in blast_file.

Optionally, flag --synteny will highlight all the syntenic blocks in this dot plot.

[Liuyunlong]

Orz,It's very very helpful.And if I want to show MCscan pairwise alignment result rather than a fast synteny scan,what could I do? Or just to transform the MCscan result to blast m8 like format ,is also can meet my job's requirement

[Liuyunlong]

It's very very helpful.And if I want to show MCscan pairwise alignment result rather than a fast synteny scan,what could I do? Or just to transform the MCscan result to blast m8 like format ,also can meet my job's requirement，thanks very much.谢谢

[Liuyunlong]

Readme of quota-alignment make me understand more clearly:)

Answer 2

[Neilfws]

The MUMmer package can generate a variety of genome-scale alignments (including translated nucleic acid sequence, using promer). It also has several plotting options: see mummerplot on the examples page for a dotplot-like example.

Answer 3

[Nakao]

LAST has a script last-dotplot.py. See also http://last.cbrc.jp/doc/last-scripts.txt and http://last.cbrc.jp/doc/last-manual.txt.

Answer 4

[Khader Shameer]

You may try polydot or dotpath from EMBOSS suite.

Answer 5

[Pierre Lindenbaum]

googling for 'dotplot' returns many command-line programs: e.g: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps

[Neilfws]

I think most of the EMBOSS apps (dotmatcher, dotpath, dottup) only plot 2 sequences against each other.

Answer 6

[Michael]

EMBOSS alignment dotplot tools: http://emboss.sourceforge.net/apps/cvs/emboss/apps/alignment_dot_plots_group.html

Answer 7

[krassowski.michal]

We wrote this small python script: https://pypi.python.org/pypi/dotplot/ which provides both CLI and GUI, although it is sequence based:

Answer 8

[lessismore]

look here
https://stackoverflow.com/questions/30060000/how-to-combine-scales-for-colour-and-size-into-one-legend

Answer 9

[toheitka]

Maybe you'll enjoy FlexiDot: It is well documented, implemented in Python and controlled with the commandline. It allows all-against-all, pairwise and self dotplots, and comes with many features, such as

• Combination of structural annotations (gff3) with dotplots, or
• LCS similarity shading and custom matrix dotplots

Code on github: http://github.com/molbio-dresden/flexidot

Publication: http://doi.org/10.1093/bioinformatics/bty395